Feebas can be encountered on Route 119 in Ruby/Sapphire/Emerald (that weird only in 6 spots thing), but I think that's still an encounter. Right now it looks like there are no encounters listed for Feebas in Gen IV and below
Fossil Pokemon (Lileep/Cradily)
Just as the starter in Ruby/Sapphire/Emerald have an "encounter location" even tho they are special, I think that would apply to these as well. You can get both in Emerald, but have to pick one or the other in Ruby/Sapphire. So I'm not sure exactly how that would be represented here.
Missing a few valid encounters
Feebas
Feebas can be encountered on Route 119 in Ruby/Sapphire/Emerald (that weird only in 6 spots thing), but I think that's still an encounter. Right now it looks like there are no encounters listed for Feebas in Gen IV and below
Fossil Pokemon (Lileep/Cradily)
Just as the starter in Ruby/Sapphire/Emerald have an "encounter location" even tho they are special, I think that would apply to these as well. You can get both in Emerald, but have to pick one or the other in Ruby/Sapphire. So I'm not sure exactly how that would be represented here.